(v3.0.1.9116) New sir_combine() for combination therapy as one engine for antibiogram(), wisca(), count_*() and proportion_*() (#321), and make all suggested packages runtime-only with a new CI workflow without dplyr

- New sir_combine() to combine SIR results of multiple antimicrobials into one variable; antibiogram(), wisca() and the count/proportion functions now use the same engine (antibiogram() and wisca() output unchanged)
- With multiple antimicrobials, count_*() and proportion_*() now follow the documented combination therapy rules: resistance() is the proportion of failing combinations, count_all() excludes isolates with an unknown combination result, and WT/NWT/NS/NI are handled correctly
- where() is now decided at runtime instead of at installation, fixing antibiogram() and wisca() without tidyselect (e.g. CRAN binaries without dplyr)
- Imports from data.table and cli moved to .onLoad(); data.table functions are only used while it is loaded; the like() example no longer unloads data.table, which crashed R
- Static test that fails on code outside functions depending on suggested packages
- New check-without-dplyr workflow: installs AMR with all suggested packages, removes dplyr (and tidyselect), then runs all unit tests and examples against the installed package
- g.test() now returns the degrees of freedom as 'parameter', so they are printed
- Fix R CMD check NOTEs (hidden .claude folder, lost braces in inherited g.test and ggplot_pca docs)

.github/scripts/test_installed_without.R

@@ -0,0 +1,91 @@
+# ==================================================================== #
+# TITLE:                                                               #
+# AMR: An R Package for Working with Antimicrobial Resistance Data     #
+#                                                                      #
+# SOURCE CODE:                                                         #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# PLEASE CITE THIS SOFTWARE AS:                                        #
+# Berends MS, Luz CF, Friedrich AW, et al. (2022).                     #
+# AMR: An R Package for Working with Antimicrobial Resistance Data.    #
+# Journal of Statistical Software, 104(3), 1-31.                       #
+# https://doi.org/10.18637/jss.v104.i03                                #
+#                                                                      #
+# Developed at the University of Groningen and the University Medical  #
+# Center Groningen in the Netherlands, in collaboration with many      #
+# colleagues from around the world, see our website.                   #
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR data analysis: https://amr-for-r.org              #
+# ==================================================================== #
+
+# Run all unit tests and all examples against the INSTALLED AMR package, in a library where some suggested packages are not available.
+# Used by .github/workflows/check-without-dplyr.yaml; run from the root of the repository:
+#   Rscript .github/scripts/test_installed_without.R dplyr tidyselect
+# The package must have been installed BEFORE the listed packages were made unavailable, as binary packages from CRAN are built on machines that have all suggested packages: code that depends on what was available at installation (instead of at runtime) then fails, which R CMD check cannot detect as it reinstalls the package.
+
+unavailable <- commandArgs(trailingOnly = TRUE)
+if (length(unavailable) == 0) {
+  stop("provide the package(s) that must be unavailable, e.g.: Rscript test_installed_without.R dplyr tidyselect")
+}
+still_available <- unavailable[vapply(unavailable, requireNamespace, logical(1), quietly = TRUE)]
+if (length(still_available) > 0) {
+  stop("these packages must not be available, but are: ", paste(still_available, collapse = ", "))
+}
+cat("Not available:", paste(unavailable, collapse = ", "), "\n")
+cat("AMR", format(utils::packageVersion("AMR")), "installed in", find.package("AMR"), "\n\n")
+
+Sys.setenv(NOT_CRAN = "true")
+library(AMR)
+
+# 1. all unit tests, against the installed package
+cat("== Unit tests ==\n")
+results <- as.data.frame(testthat::test_dir(
+  "tests/testthat",
+  package = "AMR",
+  load_package = "installed",
+  reporter = "summary",
+  stop_on_failure = FALSE
+))
+n_failed <- sum(results$failed) + sum(results$error)
+cat("\nTests: ", sum(results$nb), " expectations, ", sum(results$failed), " failed, ", sum(results$error), " errored, ", sum(results$skipped), " skipped\n", sep = "")
+
+# 2. all examples, including \donttest{} (not \dontrun{}), against the installed package
+cat("\n== Examples ==\n")
+rd_db <- tools::Rd_db("AMR")
+failed_examples <- character(0)
+n_examples <- 0
+for (rd in sort(names(rd_db))) {
+  ex_file <- tempfile(fileext = ".R")
+  tools::Rd2ex(rd_db[[rd]], ex_file, commentDonttest = FALSE)
+  if (!file.exists(ex_file)) next
+  n_examples <- n_examples + 1
+  # print the name first, so that a crash of R itself shows which help page caused it
+  cat(rd, "\n")
+  ok <- tryCatch(
+    {
+      utils::capture.output(suppressMessages(suppressWarnings(source(ex_file, local = new.env(parent = globalenv()), echo = FALSE))))
+      TRUE
+    },
+    error = function(e) {
+      cat("FAILED: ", rd, ": ", conditionMessage(e), "\n", sep = "")
+      FALSE
+    }
+  )
+  if (!ok) failed_examples <- c(failed_examples, rd)
+  grDevices::graphics.off()
+}
+cat("Examples: ", length(failed_examples), " of ", n_examples, " help pages failed\n", sep = "")
+
+if (n_failed > 0 || length(failed_examples) > 0) {
+  stop(n_failed, " test(s) failed and ", length(failed_examples), " example(s) failed without ", paste(unavailable, collapse = " and "), call. = FALSE)
+}
+cat("\nAll tests and examples passed without ", paste(unavailable, collapse = " and "), ".\n", sep = "")